Genome sequencing: Long reads for a short plant

Acipenserid herpesvirus 2 genome and partial validation of a qPCR for its detection in white sturgeon Acipenser transmontanus

White sturgeon Acipenser transmontanus is the primary species used for caviar and sturgeon meat production in the USA. An important pathogen of white sturgeon is acipenserid herpesvirus 2 (AciHV-2). In this study, 4 archived isolates from temporally discrete natural outbreaks spanning the past 30 yr were sequenced via Illumina and Oxford Nanopore Technologies platforms. Assemblies of approximately 134 kb were obtained for each isolate, and the putative ATPase subunit of the terminase gene was selected as a potential quantitative PCR (qPCR) target based on sequence conservation among AciHV-2 isolates and low sequence homology with other important viral pathogens. The qPCR was repeatable and reproducible, with a linear dynamic range covering 5 orders of magnitude, an efficiency of approximately 96%, an R2 of 0.9872, and an analytical sensitivity of 103 copies per reaction after 35 cycles. There was no cross-reaction with other known viruses or closely related sturgeon species, and no inhibition by sturgeon DNA. Clinical accuracy was assessed from white sturgeon juveniles exposed to AciHV-2 by immersion. Viral culture (gold standard) and qPCR were in complete agreement for both cell culture negative and cell culture positive samples, indicating that this assay has 100% relative accuracy compared to cell culture during an active outbreak. The availability of a whole-genome sequence for AciHV-2 and a highly specific and sensitive qPCR assay for detection of AciHV-2 in white sturgeon lays a foundation for further studies on host-pathogen interactions while providing a specific and rapid test for AciHV-2 in captive and wild populations.

Satellite-based application in drought disaster assessment using terra MOD13Q1 data across free state province, South Africa

Terra MOD13Q1 satellite data were used to assess drought disaster events and its spatiotemporal patterns over the Free State Province, South Africa between 2001 and 2019. Moderate Resolution Imaging Spectroradiometer (MODIS) products and climate data downloaded from Application for Extracting and Exploring Analysis Ready Samples" (AppEEARS) and NASA: Prediction of Worldwide Energy Resource databases, respectively were used in the study area. After acquiring MODIS data with the area of interest extracted using field sample and the layers of interest: using Enhanced Vegetation Index (EVI) and pixel reliability and defining the output as GeoTIFF with geographic projection, R programming was used for the analysis. This study also evaluated Standardized Precipitation Index (SPI) to further identify meteorological drought, computed at various time scales utilising information acquired from the Global Drought Observatory database. The results show and identify the years that are water-stressed in the study area, which indicated that low vegetation abundance and high temperature in the Free State Province occurred in 2000, 2008, and 2009. The result also shows that the summer season over large parts of the study region is characterized by moderate to extreme drought while winter seasons have light drought conditions during the same time. Seasonal and inter-annual comparisons of drought events outlined in the Vegetation Condition Index (VCI) provided a useful tool for analysing the temporal and spatial evolution of regional drought and for estimating potential environmental impacts. Drought events occurrence in the study area is less frequent and milder in winter months while summer droughts of different years were more severe. The results of this study can also be used as a tool for monitoring droughts and support for decision making in the evaluation and management of regional drought, for disaster preparedness.

Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids

Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homeologs in natural polyploids is largely unknown. To study this expression balance, the expression patterns of 2180 structurally well-characterized genes of wheat were studied, of which 813 had the expected three copies and 375 had less than three. Copy numbers of the remaining 992 ranged from 4 to 14, including homeologs, orthologs, and paralogs. Of the genes with three structural copies corresponding to homeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies. Homeologs of 76-87% of the genes showed differential expression patterns in different tissues, thus have evolved different gene expression controls, possibly resulting in novel functions. Homeologs of 55% of the genes showed tissue-specific expression, with the largest percentage (14%) in the anthers and the smallest (7%) in the pistils. The highest number (1.72/3) of homeologs/gene expression was in the roots and the lowest (1.03/3) in the anthers. As the expression of homeologs changed with changes in structural copy number, about 30% of the genes showed dosage dependence. Chromosomal location also impacted expression pattern as a significantly higher proportion of genes in the proximal regions showed expression from all three copies compared to that present in the distal regions.

Homoeologs: What Are They and How Do We Infer Them?

The evolutionary history of nearly all flowering plants includes a polyploidization event. Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature. With several allopolyploid genome sequencing projects under way, there is a pressing need for computational methods for homoeology inference. Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs. In the second part, we survey experimental and computational methods of homoeolog inference, considering the strengths and limitations of each approach. Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization.